Merge branch 'master' into packin

Author: adamnovak

.dockerignore

@@ -1,4 +1,3 @@
 Dockerfile
-.git
 .dockerignore
 Brewfile

.github/ISSUE_TEMPLATE/report-a-bug.md

@@ -0,0 +1,43 @@
+---
+name: Report a Bug
+about: Report a bug that causes vg to crash or otherwise behave incorrectly
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+<!--
+Please answer the following questions about your bug.
+
+If you copy commands or output from your terminal, please place the text in its own paragraph, surrounded by lines of three backticks.
+
+```
+Like this.
+```
+
+-->
+
+**1. What were you trying to do?**
+
+
+**2. What did you want to happen?**
+
+
+**3. What actually happened?**
+
+
+**4. If you got a line like `Stack trace path: /somewhere/on/your/computer/stacktrace.txt`, please copy-paste the contents of that file here:**
+
+```
+Place stacktrace here.
+```
+
+**5. What data and command can the vg dev team use to make the problem happen?**
+
+
+**6. What does running `vg version` say?**
+
+```
+Place vg version output here
+```

.github/ISSUE_TEMPLATE/support-request.md

@@ -0,0 +1,14 @@
+---
+name: Support Request
+about: Get help installing or using vg, or get questions answered
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**PLEASE DO NOT MAKE SUPPORT REQUESTS HERE**
+
+Please the Biostars forum instead:
+
+https://www.biostars.org/new/post/?tag_val=vg

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,6 @@
+## Changelog Entry
+To be copied to the [draft changelog](https://github.com/vgteam/vg/wiki/Draft-Changelog) by merger:
+
+ * Whatsits now frobnicated
+
+## Description

.github/workflows/testmac.yml

@@ -0,0 +1,78 @@
+name: Test Mac
+
+# Run on our main branch and any PRs to it, and on release tags, but not every
+# commit in every branch.
+on:
+  push:
+    branches:    
+      - master
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  testmac:
+    name: Test on Mac
+    runs-on: macos-12
+
+    steps:
+      - name: Use cache
+        uses: actions/cache@v2
+        with:
+          path: | 
+            deps
+            lib
+            include
+            bin
+          key: ${{ runner.os }}-12-${{ github.ref }}
+          # Restore keys are a "list", but really only a multiline string is
+          # accepted. Also we match by prefix. And the most recent cache is
+          # used, not the most specific.
+          # See: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
+          restore-keys: |
+            ${{ runner.os }}-12-${{ github.base_ref }}
+            ${{ runner.os }}-12
+          
+      - name: Checkout code without submodules
+        uses: actions/checkout@v2
+      
+      - name: Get or restore dependencies
+        run: scripts/restore-deps.sh
+       
+      - name: Install packages
+        # We don't use artemnovichkov/action-homebrew because that's for Linux.
+        # We uninstall everything we don't need in order to prevent linking
+        # conflicts with existing/outdated packages, which we can't resolve
+        # because there's no way to tell Homebrew to force-link when installing
+        # from a Brewfile. We also update Protobuf to make sure we have 3.21.3+
+        # to avoid problems with ABI changes with/without -DNDEBUG.
+        # And we update libomp to make extra sure it will be picked up by the compiler.
+        # We pre-install a pinned txm to work around https://github.com/anko/txm/issues/8
+        run: |
+          brew bundle cleanup --force && \
+          brew bundle install && \
+          brew update && \
+          brew install protobuf && \
+          brew install libomp && \
+          npm install -g txm@7.4.5 && \
+          brew config && \
+          (brew doctor || echo "brew doctor is unhappy")
+
+      - name: Run build and test
+        run: |
+          export VG_FULL_TRACEBACK=1
+          echo "Build with $(nproc) threads"
+          set +e
+          make -j$(nproc) test
+          RETVAL=$?
+          set -e
+          # Whether vg testing succeeds or fails, see if we can get any Apple crash logs for it.
+          ls ~/Library/Logs/DiagnosticReports/
+          for CRASH_FILE in $(ls ~/Library/Logs/DiagnosticReports/vg-* 2>/dev/null) ; do
+              echo "vg crash report found: ${CRASH_FILE}"
+              cat ${CRASH_FILE}
+          done
+          exit $RETVAL
+        shell: bash

.gitignore

@@ -23,6 +23,7 @@ test/*/*.lcp
 test/**/*.index/
 trash
 src/*.gch
+.vscode
 # Ignore a bunch of files people might dump in the root when testing
 /*.vg
 /*.gcsa
@@ -42,3 +43,4 @@ src/*.gch
 /*.svg
 /*.fa
 /*.gfa
+.vscode/*